It's fortunate you're getting an engine done under warranty with the FuelPak installed. That alone might be a good reason not to rock the boat while they're getting the work done.
The amount of carbon buildup necessary to ruin an engine in as few miles as described is.... well... surprising. I could be convinced to question the FuelPak there as much as I might the fuel itself. After the fact, and without in use tracking of any kind, you're not going to be able to say for sure anyway. So take the warranty work, smile, declare victory, tweak a little to your riding style (if they'll let you as part of the warranty repair), and ride on.
I'm a fan of the Andrews 48 mentioned above. It matches well to what you described as a riding style. With everything done with that in mind it makes my Road King and I a very satisfied rider.